The principal objective of this study is to elucidate metabolic and biological functions of polyunsaturated fatty acids, docosahexaenoic acid (22:6n3) and arachidonic acid (20:4n6) in the nervous system with particular reference to their modulation by ethanol. We have previously found that 22:6n3 promotes the accumulation of phosphatidylserine (PS), which is thought to be involved in growth factor signaling leading to cell survival. Preliminary results obtained by the differential sedimentation assay indicated that polyunsaturated fatty acids, 20:4n6 and 22:6n3, prevented the apoptotic cell death of both Neuro 2A and PC-12 cells. During this period, the effect of polyunsaturates on the survival of neuronal cells was further investigated along with the underlying mechanisms of this effect. The apoptotic cell death induced by serum deprivation was confirmed by DNA ladder formation and by Hoechst staining. Docosahexaenoic acid significantly decreased DNA ladder formation and chromatin condensation. However, 22:6n3 exerted its effect only after enrichment of this fatty acid in membrane phospholipids, especially in the aminophospholipids, phosphatidylethanolamine (PE) and phosphatidylserine (PS). These data suggest that 22:6n3 as a membrane phospholipid constituent, especially in aminophospholipids, may be important for the protective effect. The analysis by RT-PCR and immunoblotting indicated that the prevention of apoptosis by 22:6n3 enrichment was mediated by the down regulation of CPP-32 at both gene and protein levels but not by over expression of bcl-2. We also found during this period that n-3 deficiency decreased melatonin biosynthesis significantly, suggesting a role of n-3 polyunsaturated fatty acids in pineal biochemical functions.